modelfree-protein15n 0.0.5

Model free analysis of protein backbone amide 15N spin relaxation rates.

# modelfree-protein15n Model-Free analysis framework for protein backbone amide 15N NMR spin relaxation rates.

This tool fits the relaxation data to a multi-Lorentzian spectral density function. One can choose the number of Lorentzians (dynamic modes) for the fit. Typically, one can perform 1, 2, and 3 dynamic mode MF analysis and see which model is most relevant for the data. IMPACT analysis is also possible by fixing the correlation times and fitting the amplitudes.

## Relevant litterature

Lipari & Szabo, Journal of the American Chemical Society (1982); Halle, The Journal of chemical physics (2009); Khan et al., Biophysical journal (2015)

# installation

$ pip install modelfree-protein15n

# usage

The program is able to generate random relaxation data with the command ‘modfree generate’. The program is able to fit relaxation data to a model with the command ‘modfree fit’. The program is able to plot the results with the command ‘modfree plot’.

## Data generation

To generate relaxation data, type the following command:

$ modfree generate

The following flags are available: -o (str): Output directory containing the generated data. -modes (int): number of dynamic modes used to generate the data -n (int): number of residues in the data -noise (float): between 0 and 1, indicates the proportion of noise to put in the data. (0.03 by default) -fields (list, int or float): Magnetic fields used for the rate generation in MHz. -rates: relaxation rates to generate. by default R1, R2, NOE, etaXY.

For example, you can type:

$ modfree generate -o Generated -modes 2 -n 70 -noise 0.05 -fields 600 700 850 950 1200 -rates R1 R2 NOE etaXY etaZ

## Data fitting

To fit relaxation data, you will need your data in a specific format akin to the generated data. Generate some data to see how it’s done. You will also need a directory file and a parameter file. type the following command to fit the data generated in the previous section:

$ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml

You can also fit only part of the data with the flag -r:

$ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml -r 10 11 12 13 14 15 16 17

Or

$ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml -r 15

## Data plotting

To plot the fitted data, just type:

$ modfree plot -o Generated_fit -p all

The following flags are available: -o (str): Output directory containing the data. -p: What to plot (all, relaxation, parameters, statistics, correlation) -format: Format of the plot files (pdf, png, jpg, svg…) -dpi (600 by default)